GEO DataSets

(Submitter supplied) The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance. By comparing the low temperature transcriptomes of the IT and SW ecotypes with the CBF pathway being knocked out, we showed the CBF pathway plays a significant role in natural variation of freezing tolerance.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

44 Samples

Download data: CSV

(Submitter supplied) The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance. By comparing the low temperature transcriptomes of the IT and SW ecotypes, we showed CBF pathway plays a significant role in natural variation of freezing tolerance.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

18 Samples

Download data: CSV

(Submitter supplied) Gene expression Arabidopsis 24h cold-treated, 4c, seedlings to identify a *gold-standard* set of cold-responsive transcripts. Most of the CBF overexpression lines are in WS, therefore, it is necessary to identify a consistent set of transcripts that are detectible as cold-induced on the ATH1 platform for both WS and Columbia, so that appropriate comparisons can be made to determine the effects of low temperature in CBF overexpressing or loss of function plants in a WS background and an attempt can be made to compare the results of altered CBF function to published microarray studies. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

9 Samples

Download data: CEL

(Submitter supplied) Our goal in this study is to understand the regulation mechanism of genes including CBF regulon in low temperature. We addressed these issues by overexpressing the transcription factors encoded by genes that are rapidly induced in parallel with the CBF genes. The results show that the low temperature regulatory network is highly interconneted.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

28 Samples

Download data: CEL

(Submitter supplied) CBF1, CBF2 and CBF3 regulons comprise nearly identical gene sets The vast majority of CBF2 regulon genes were down-regulated less that 50% by overexpression of CBF2Δc, a truncated version of CBF2

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

28 Samples

Download data: CEL

(Submitter supplied) In Arabidopsis, CBFs transcription factors (CBF1, CBF2 and CBF3) play fundamental roles in plant cold tolerance, especially in cold-acclimation. By employing CRISPR/Cas9, we knocked out CBF1 and CBF2 simultaneously in cbf3 background and generated cbfs triple mutant. This mutant facilitated the discovery of CBF-regulated genes. In this study, Arabidopsis 14-d-old Col-0 and cbfs mutant were treated with cold stress (4 degree centigrade) for 0, 3 and 24 hours. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

12 Samples

Download data: TXT

(Submitter supplied) Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL16226

207 Samples

Download data: XYS

(Submitter supplied) St (common potato) is a freezing sensitive species unable to cold acclimate. The close wild relative Sc is freezing tolerant and able to cold acclimate. Here we compare the cold transcriptome of these two species with different levels of freezing tolerance. We also identify the putative CBF regulons by comparing the transcriptomes of wild type plants with that of 35S::AtCBF3 transgenic lines in both species.

Organism:

Solanum commersonii; Solanum tuberosum

Type:

Expression profiling by array

Platform:

GPL10564

8 Samples

Download data: GPR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL9020 GPL198

24 Samples

Download data: CEL, TXT

(Submitter supplied) The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

12 Samples

Download data: TXT

(Submitter supplied) Salicylic acid (SA) levels increase in Arabidopsis upon exposure to low temperature for more than a week. This cold-induced SA biosynthesis was found to proceed through the isochorismate synthase (ICS) pathway. The sid2-1 mutant is deficient in ICS1 and does not make SA at low temperature. We used microarray analysis to examine the genes differentially regulated by low temperature that were dependent on SA

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) CAMTA3 is known to be involved in regulation of induction of early cold-responsive genes, CBF1 and CBF2 at cold conditions and of suppression of SA production at warm temperature. Considering a functional redundancy of CAMTA family members in both warm and cold conditions, high-order of camta mutants, camta double and triple mutants, were generated and used to determined the effects of their regulation using microarray analysis.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

21 Samples

Download data: CEL

(Submitter supplied) To understand the role of Arabidopsis histone deacetylase HDA6 in plant cold acclimation, we have employed transcriptional profiling of the hda6 mutant and its parental line under cold and control conditions to identify genes differentially expressed in the hda6 mutant under cold and control conditions. Aligent’s Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K) were used.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

12 Samples

Download data: TXT

(Submitter supplied) The purpose of this experiment was to identify genes responding differently to a 24 h low red to far red ratio (R:FR) treatment in plants grown at 16 and 22 degrees Keywords: Light treatment

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

4 Samples

Download data: CEL

(Submitter supplied) To understand the role of STCH4 in cold-responsive gene regulation

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

18 Samples

Download data: TXT

(Submitter supplied) Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under cold stress to identify transcripts which are mis-spliced/intron-retained in rcf1-1.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL10977

6 Samples

Download data: CEL, TXT

(Submitter supplied) Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under normal growth conditions to identify transcripts which are mis-spliced/intron-retained in rcf1-1.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL10977

6 Samples

Download data: CEL, TXT

(Submitter supplied) Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified an essential regulator of cold-responsive genes and used the Affymetrix whole-genome arrays to define downstream targets of this important protein. We used the microarrays to reveal the effect of rcf1-1 mutation on global gene expression with or without cold stress at 4°C. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) The sfr6-1 mutant of Arabidopsis has been shown to be defective in freezing tolerance and fails to express a number of cold-regulated genes to normal wild type levels. The aim of this experiment was to test whether two other mutant alleles, sfr6-2 and sfr6-3 showed similar defects in cold-inducible gene expression.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

4 Samples

Download data: CEL